{"action":"created","comment":{"url":"https://api.github.com/repos/greenelab/deep-review/pulls/comments/99042933","pull_request_review_id":19702766,"id":99042933,"diff_hunk":"@@ -52,7 +52,104 @@ particularly notable in this area?*\n \n ### Protein secondary and tertiary structure\n \n-*Jinbo Xu is writing this*\n+Proteins play fundamental roles in all biological processes including the \n+maintenance of cellular integrity, metabolism, transcription/translation, and \n+cell-cell communication. Complete description of protein structures and \n+functions is a fundamental step towards understanding biological life and \n+also highly relevant in the development of therapeutics and drugs. Tons of \n+protein sequences have been generated, but fewer than 100,000 of them \n+have experimentally-solved structures. As a result, computational structure \n+prediction is essential for a majority number of protein sequences. However, \n+predicting protein 3D structures from sequence alone is very challenging, \n+especially when similar templates are not available. In the past decades, \n+various computational methods have been developed to predict protein \n+structure from different aspects, including prediction of secondary structure, \n+torsion angles, solvent accessibility, inter-residue contact map, disorder \n+regions and side-chain packing.\n+\n+Machine learning is extensively applied to predict protein structures and \n+some success has been achieved. For example, secondary structure can be \n+predicted with about 80% of Q3 accuracy by a 2-layer neural network \n+method PSIPRED [@doi:10.1093/bioinformatics/16.4.404]. Starting from \n+2012, deep learning has been gradually introduced to protein structure \n+prediction. The adopted deep learning models include deep belief network, \n+LSTM(long short-term memory), deep convolutional neural networks (DCNN) \n+and deep convolutional neural fields[@doi:10.1007/978-3-319-46227-1_1 \n+@doi:10.1038/srep18962]. Here we focus on deep learning methods for \n+two representative subproblems: secondary structure prediction and ","path":"sections/04_study.md","position":31,"original_position":29,"commit_id":"2d94fbb951bc5f6d5e5c39eaf7630457e8f0c18f","original_commit_id":"f512c6f3ee14aecffca37ea73823ba78785fd3aa","user":{"login":"gwaygenomics","id":7340421,"avatar_url":"https://avatars.githubusercontent.com/u/7340421?v=3","gravatar_id":"","url":"https://api.github.com/users/gwaygenomics","html_url":"https://github.com/gwaygenomics","followers_url":"https://api.github.com/users/gwaygenomics/followers","following_url":"https://api.github.com/users/gwaygenomics/following{/other_user}","gists_url":"https://api.github.com/users/gwaygenomics/gists{/gist_id}","starred_url":"https://api.github.com/users/gwaygenomics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gwaygenomics/subscriptions","organizations_url":"https://api.github.com/users/gwaygenomics/orgs","repos_url":"https://api.github.com/users/gwaygenomics/repos","events_url":"https://api.github.com/users/gwaygenomics/events{/privacy}","received_events_url":"https://api.github.com/users/gwaygenomics/received_events","type":"User","site_admin":false},"body":"This being said, I do not want to stall up progress for any reason! I understand that it is often much easier to work with a full manuscript once the tone/message is clarified so if the merge was close, I'd say go for it. (right now I'm trying to get a feel of how progress through PRs is being made!)","created_at":"2017-02-02T02:24:48Z","updated_at":"2017-02-02T02:35:26Z","html_url":"https://github.com/greenelab/deep-review/pull/191#discussion_r99042933","pull_request_url":"https://api.github.com/repos/greenelab/deep-review/pulls/191","_links":{"self":{"href":"https://api.github.com/repos/greenelab/deep-review/pulls/comments/99042933"},"html":{"href":"https://github.com/greenelab/deep-review/pull/191#discussion_r99042933"},"pull_request":{"href":"https://api.github.com/repos/greenelab/deep-review/pulls/191"}}},"pull_request":{"url":"https://api.github.com/repos/greenelab/deep-review/pulls/191","id":100610741,"html_url":"https://github.com/greenelab/deep-review/pull/191","diff_url":"https://github.com/greenelab/deep-review/pull/191.diff","patch_url":"https://github.com/greenelab/deep-review/pull/191.patch","issue_url":"https://api.github.com/repos/greenelab/deep-review/issues/191","number":191,"state":"open","locked":false,"title":"the first draft for protein structure 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